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How to trim adapters from paired end FASTQ data

This recipe performs data quality control on FASTQ data downloaded from SRA.

1 result • updated 18 days ago by Istvan Albert

This recipe performs data quality control on FASTQ data downloaded from SRA.

The recipe trims Illumina sequencing adapters from the end of sequences then performs a sliding window approach for correcting trailing low-quality sequences.

Finally, quality control reports are generated with fastqc.

For more information see the

Applied Bioinformatics online course
Biostar Handbook for system setup and other information.

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# The SRR run number.
SRA={{sra.value}}

# Stop the script on errors.
set -uex

# How many sequences to unpack.
N=10000

# Create directory to store the reads in.
mkdir -p reads

# Download 1000 reads from SRA.
fastq-dump --split-files -X $N -O reads  $SRA

# Make a directory for the fastqc reports
mkdir -p reports

# Run the fastqc report on the sra reads.
fastqc reads/*.fastq -o reports

# Create the adapter sequence used for trimming.
echo ">illumina" > adapter.fa
echo "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" >> adapter.fa

# Run trimmomatic on the data.
trimmomatic PE reads/${SRA}_1.fastq reads/${SRA}_2.fastq -baseout reads/${SRA}.trimmed.fq  ILLUMINACLIP:adapter.fa:2:30:5 SLIDINGWINDOW:4:20

# Run trimmomatic on the trimmed data.
fastqc reads/*.fq -o reports

# Delete the fastqc zip files to reduce clutter.
rm -f reports/*.zip

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